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Hey Glasstapper....do you have a rotary tool? I took a grinding tool and made the hole in the clay pots bigger so that the fish could swim thru....they love it! Other than that our mbuna love loads of rocks making hundreds of little hidey holes. Hubby took a long piece of pvc pipe for along the back and stacks the rocks all over each other and the pvc. Basically, 2 pieces of "roundish" rock with a piece of "flattish" rock across the top all along the tank. About once a month he will remove the rocks during water changes and restructure them. If you choose to silicone (which honestly I wish he would, I have nightmares about these darn rocks tumbling down in the middle of the night breaking the tank) silicone them in small enough structures that you can move them around or in and out. It gives you more stability, but still easy to deal with.
Good luck, the tank should be quite colorful when done!

Ok, that's pretty much what I want to do here. I don't have any way of making the hole any bigger, but that's something I could always do later on. I'm not really understanding the pvc, though. Is it to help hold the structure up or is it another cave for the fish?

The PVC is another cave or series of caves. I can't even begin to think about taking all of the rocks out of my tank. Just the thought of it makes my back hurt. Rocks are great and look natural but PVC pipe is much easier to work with. Make sure to show us pictures when you are done.

The pvc acts as both.....we frequently see the fish swimming in and out of the pipe and they also offer something to start stacking the rocks on, lay against, etc. that creates additional hidey places.
If you know anyone with a dremel rotary tool ask to borrow it, buy a grinding stone and work away at those holes. I have also heard of people using a hammer and "knocking" pieces out of the pots to make entrances, but my luck I would smash the whole thing to smithereens and have to go buy more. The rock glued on looks great.

Well, I think I'll add the pvc later on because I'll want to glue rocks on those, too. Those pots are coming along nicely, but the rock glueing takes a while and some pieces along the edges especially have to be individually hand placed. That silicone stinks to high heaven, but it's doing a wonderful job. I did knock out the bottoms of the pots with a flathead screwdriver and a hammer. It was actually pretty easy if you go slow. I'll finish the rock glueing and let them sit for a couple of days before I place everything in there. I'll definitely post some pictures for you guys!